At the moment I use the following sequence: when in phasing orbit, fire up Precession MFD, push TGT, enter target's name. Set NOR to say 20 to see if your closest approach comes within the next 20 orbits. If inclination is more or less aligned, the closest approach will be on the order of altitude difference between you and the target. Then press WAK, enter number of orbits to intercept minus 3 or 2 (let's say "17 revs"), set high time acceleration and wait till you are woken up by Precession MFD. Then, for the actual burn, the easiest way is to use IMFD. Set Target Intercept, enter target name, set TIn with SET button to approximately the time to intercept shown in Precession MFD, vary TEj and TIn to get the lowest total dV, and do the ejection burn within IMFD.
Afterwards, power off IMFD and bring up Burn Time Calculator. Set Target, set offset to your desired standoff distance. In Precession MFD after IMFD burn the closest approach will be on the order of a few kilometers, set NOR to 0.5 (assuming you're half an orbit from the rendezvous), and set OFF to whatever aimpoint you need - if you're arriving ahead of the target (V-bar), set 0 300 0.
Now use RCS in linear mode to null closest approach distance that shows in the top line. Once you've done that (and be prepared for further minor corrections along the way), note the dV value from Precession MFD and enter it into Burn Time Calculator, then press ARM. Once that is done, you can use PITCH UP/DOWN, YAW LEFT/RIGHT indications from the bottom line to orient for rendezvous burn.
Oh, and by the way. The minimum realistic miss distance that shows up in the screen is on the order of 0.3-0.8 meters, finetuning by RCS with Ctrl key pressed down.
It also makes sense to reduce NOR value as intercept time nears, since sometimes the optimizer locks on the wrong local minimum, from the initial guess at the middle of the interval.